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- PDB-6xqp: Structure of human D462-E4 TCR in complex with human MR1-5-OP-RU -

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Basic information

Entry
Database: PDB / ID: 6xqp
TitleStructure of human D462-E4 TCR in complex with human MR1-5-OP-RU
Components
  • Beta-2-microglobulin
  • Major histocompatibility complex class I-related gene protein
  • TRAV12-2 alpha chain
  • TRBV29-1
KeywordsIMMUNE SYSTEM / MAIT / MR1 / Metabolite presentation
Function / homology
Function and homology information


positive regulation of T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of exogenous antigen / MHC class I receptor activity / beta-2-microglobulin binding / T cell receptor binding / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression ...positive regulation of T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of exogenous antigen / MHC class I receptor activity / beta-2-microglobulin binding / T cell receptor binding / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / protein homotetramerization / defense response to Gram-negative bacterium / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / external side of plasma membrane / Golgi membrane / innate immune response / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set ...MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Chem-2LJ / BROMIDE ION / Beta-2-microglobulin / Major histocompatibility complex class I-related gene protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsAwad, W. / Rossjohn, J.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Atypical TRAV1-2 - T cell receptor recognition of the antigen-presenting molecule MR1.
Authors: Awad, W. / Meermeier, E.W. / Sandoval-Romero, M.L. / Le Nours, J. / Worley, A.H. / Null, M.D. / Liu, L. / McCluskey, J. / Fairlie, D.P. / Lewinsohn, D.M. / Rossjohn, J.
History
DepositionJul 10, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 28, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Major histocompatibility complex class I-related gene protein
B: Beta-2-microglobulin
C: Major histocompatibility complex class I-related gene protein
D: Beta-2-microglobulin
E: TRAV12-2 alpha chain
F: TRBV29-1
G: TRAV12-2 alpha chain
H: TRBV29-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,65424
Polymers188,0528
Non-polymers1,60216
Water5,963331
1
A: Major histocompatibility complex class I-related gene protein
B: Beta-2-microglobulin
E: TRAV12-2 alpha chain
F: TRBV29-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,70011
Polymers94,0264
Non-polymers6747
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9620 Å2
ΔGint-80 kcal/mol
Surface area35120 Å2
MethodPISA
2
C: Major histocompatibility complex class I-related gene protein
D: Beta-2-microglobulin
G: TRAV12-2 alpha chain
H: TRBV29-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,95413
Polymers94,0264
Non-polymers9289
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10260 Å2
ΔGint-73 kcal/mol
Surface area35580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.877, 113.433, 209.606
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 4 types, 8 molecules ACBDEGFH

#1: Protein Major histocompatibility complex class I-related gene protein / MHC class I-related gene protein / Class I histocompatibility antigen-like protein


Mass: 31711.670 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MR1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q95460
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#3: Protein TRAV12-2 alpha chain


Mass: 22740.104 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#4: Protein TRBV29-1


Mass: 27694.844 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Non-polymers , 6 types, 347 molecules

#5: Chemical ChemComp-2LJ / 1-deoxy-1-({2,6-dioxo-5-[(E)-propylideneamino]-1,2,3,6-tetrahydropyrimidin-4-yl}amino)-D-ribitol / 5-(2-oxopropylideneamino)-6-D-ribitylaminouracil


Mass: 316.310 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H20N4O6 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#8: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#9: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 331 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.22 Å3/Da / Density % sol: 61.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 18-26% PEG3350, 100 mM Bis-Tris Propane 200 mM Sodium Bromide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.9→45.81 Å / Num. obs: 54572 / % possible obs: 99.92 % / Redundancy: 2 % / Biso Wilson estimate: 43.56 Å2 / CC1/2: 0.99 / Net I/σ(I): 10.11
Reflection shellResolution: 2.9→3 Å / Num. unique obs: 5362 / CC1/2: 0.513

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4L4T

4l4t


Resolution: 2.9→45.81 Å / SU ML: 0.3463 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.2602
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.235 2819 5.17 %
Rwork0.1904 51750 -
obs0.1927 54569 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.58 Å2
Refinement stepCycle: LAST / Resolution: 2.9→45.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12465 0 93 331 12889
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003112949
X-RAY DIFFRACTIONf_angle_d0.607417605
X-RAY DIFFRACTIONf_chiral_restr0.04111889
X-RAY DIFFRACTIONf_plane_restr0.00392328
X-RAY DIFFRACTIONf_dihedral_angle_d21.22184658
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.950.33591530.27452541X-RAY DIFFRACTION100
2.95-30.33491380.27042530X-RAY DIFFRACTION100
3-3.060.28431350.25352566X-RAY DIFFRACTION99.96
3.06-3.120.30291560.24522548X-RAY DIFFRACTION100
3.12-3.190.33971330.24592564X-RAY DIFFRACTION99.93
3.19-3.270.31311370.23742543X-RAY DIFFRACTION100
3.27-3.350.25581200.21952577X-RAY DIFFRACTION99.96
3.35-3.440.26121490.2022551X-RAY DIFFRACTION100
3.44-3.540.23581480.18742568X-RAY DIFFRACTION99.96
3.54-3.650.23121300.17892587X-RAY DIFFRACTION100
3.65-3.780.24861540.1772558X-RAY DIFFRACTION100
3.78-3.940.22021330.18082575X-RAY DIFFRACTION99.96
3.94-4.110.21171500.16952578X-RAY DIFFRACTION99.96
4.11-4.330.17741420.14492564X-RAY DIFFRACTION100
4.33-4.60.18171200.13522614X-RAY DIFFRACTION99.96
4.6-4.960.1681250.1392623X-RAY DIFFRACTION100
4.96-5.450.2131360.15382612X-RAY DIFFRACTION99.93
5.46-6.240.1961570.18832611X-RAY DIFFRACTION99.96
6.24-7.860.25121440.21552673X-RAY DIFFRACTION99.93
7.86-45.810.22121590.21182767X-RAY DIFFRACTION99.66
Refinement TLS params.Method: refined / Origin x: 5.7933 Å / Origin y: 21.0148 Å / Origin z: -20.5078 Å
111213212223313233
T0.04798 Å20.0016 Å20.0041 Å2-0.0512 Å20.022 Å2--0.0414 Å2
L0.0499 °2-0.017 °20.032 °2-0.0159 °20.0081 °2--0.0449 °2
S0.0124 Å °0.0475 Å °-0.0472 Å °-0.0045 Å °-0.0066 Å °0.0087 Å °-0.0078 Å °0.01607 Å °0 Å °
Refinement TLS groupSelection details: all

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